The ocean contains a complex food web–the network of interactions among predators and prey that maintain healthy ecosystems and support populations of aquatic animals. At the base of this web are plants and simple, small organisms like phytoplankton or protists, a group of single-celled organisms that includes amoeba and algae. Giant viruses can have a significant influence on protists, and can help trigger events like major algae blooms that have many negative impacts on marine ecosystems. As such, scientists are trying to learn more about these giant viruses. If we know which viruses can cause huge algae blooms, we may be able to prepare or prevent these serious problems.
A new study has reported the discovery of 230 new giant ocean viruses, and the sequences of these DNA viruses have been deposited in public databases. The researchers also characterized many of the viral genes, and revealed 530 novel, functional viral proteins from these genomes. The characterizations of some viral proteins indicated that giant viruses may be able to alter host cell processes and functions. The work has been reported in npj Viruses.
"Giant viruses are often the main cause of death for many phytoplankton, which serve as the base of the food web supporting ocean ecosystems and food sources. The novel functions found in giant viruses could have biotechnological potential, as some of these functions might represent novel enzymes," noted senior study Mohammad Moniruzzaman, an assistant professor at the Rosenstiel School of Marine, Atmospheric and Earth Science at the University of Miami.
Advances in genetic and computational tools in recent decades have made work on giant viruses possible. With metagenomics, researchers can collect a sample of something like soil, or ocean water, for example, and then sequence all of the genetic material inside.
These genetic sequences can be compared to known sequences to learn more about them, or additional work may show that novel species are contained in a sample.
In this study, the scientists developed a tool called BEREN (bioinformatic tool for eukaryotic virus recovery from environmental metagenomes), which is specifically meant to identify the genomes of giant viruses in DNA sequencing datasets that are publicly available. Large metagenomes from nine DNA sampling projects were analyzed with a supercomputer that could reconstruct hundreds of libraries of microbial and viral DNA.
The genomes that were reconstructed were compared to known sequences of giant viruses, and the researches began to look for new genes and functions.
"This study allowed us to create a framework to improve existing tools for detecting novel viruses that could aid in our ability to monitor pollution and pathogens in our waterways," said first study author Benjamin Minch, a graduate candidate at the Rosenstiel School.
This work showed that there are giant virus genes that can affect cell functions like photosynthesis or metabolism. Since these types of genes are usually only found in cellular organisms, giant viruses may, therefore, be significantly affecting host metabolism during a giant virus infection, which could be affecting marine biogeochemistry in turn, added Minch.
BEREN can be downloaded for free at: gitlab.com/benminch1/BEREN
Sources: Rosenstiel School of Marine, Atmospheric, and Earth Science; npj Viruses
